de.jstacs.data.sequences.annotation

Class NullSequenceAnnotationParser

java.lang.Object

de.jstacs.data.sequences.annotation.NullSequenceAnnotationParser

All Implemented Interfaces:

SequenceAnnotationParser

public final class NullSequenceAnnotationParser
extends Object
implements SequenceAnnotationParser

This SequenceAnnotationParser returns always null as SequenceAnnotation. That is it add no SequenceAnnotation to each Sequence.

The class should be used by accessing DEFAULT_INSTANCE.

Author:

Jens Keilwagen

Field Summary

Fields

Modifier and Type	Field and Description
static NullSequenceAnnotationParser	DEFAULT_INSTANCE The only instance of this class which is publicly available.

Method Summary

Methods

Modifier and Type	Method and Description
void	addToAnnotation(String unparsed) This method adds the unparsed String in some way to the SequenceAnnotation.
void	clearAnnotation() This method reset the current SequenceAnnotation.
SequenceAnnotation[]	getCurrentAnnotation() This method returns the current SequenceAnnotation.
String	parseAnnotationToComment(char commentChar, SequenceAnnotation... annotations) This method returns a String representation of the given SequenceAnnotations that can be used as comment line in a file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_INSTANCE

public static final NullSequenceAnnotationParser DEFAULT_INSTANCE

The only instance of this class which is publicly available.

Method Detail

addToAnnotation

public void addToAnnotation(String unparsed)

Description copied from interface: SequenceAnnotationParser

This method adds the unparsed String in some way to the SequenceAnnotation.

Specified by:

addToAnnotation in interface SequenceAnnotationParser

Parameters:

unparsed - the String containing the annotation

clearAnnotation

public void clearAnnotation()

Description copied from interface: SequenceAnnotationParser

This method reset the current SequenceAnnotation.

Specified by:

clearAnnotation in interface SequenceAnnotationParser

getCurrentAnnotation

public SequenceAnnotation[] getCurrentAnnotation()

Description copied from interface: SequenceAnnotationParser

This method returns the current SequenceAnnotation.

Specified by:

getCurrentAnnotation in interface SequenceAnnotationParser

Returns:

the current SequenceAnnotation

parseAnnotationToComment

public String parseAnnotationToComment(char commentChar,
                              SequenceAnnotation... annotations)

Description copied from interface: SequenceAnnotationParser

This method returns a String representation of the given SequenceAnnotations that can be used as comment line in a file.
Normally, the method should do the opposite of SequenceAnnotationParser.addToAnnotation(String).

Specified by:

parseAnnotationToComment in interface SequenceAnnotationParser

Parameters:

commentChar - the char at the beginning of comment lines

annotations - the SequenceAnnotations to be parsed

Returns:

a String representing the given SequenceAnnotations

See Also:

DataSet.save(java.io.OutputStream, char, SequenceAnnotationParser)